PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes

Chao Qin, Ying-hui Li, Delin Li, Xueru Zhang, Lingping Kong, Yonggang Zhou, Xiangguang Lyu, Ronghuan Ji, Xiuzhi Wei, Qican Cheng, Zhiwei Jia, Xiaojiao Li, Qiang Wang, Yueqiang Wang, Wen Huang, Chunyan Yang, Like Liu, Xing Wang, Guangnan Xing, Guoyu Hu, Zhihui Shan, Ruizhen Wang, Haiyan Li, Hongyu Li, Tao Zhao, Jun Liu, Yuping Lu, Xiping Hu, Fanjiang Kong (), Li-juan Qiu () and Bin Liu ()
Additional contact information
Chao Qin: Chinese Academy of Agricultural Sciences
Ying-hui Li: Chinese Academy of Agricultural Sciences
Delin Li: Chinese Academy of Agricultural Sciences
Xueru Zhang: Purdue University
Lingping Kong: Guangzhou University
Yonggang Zhou: Hainan Yazhou Bay Seed Laboratory
Xiangguang Lyu: Chinese Academy of Agricultural Sciences
Ronghuan Ji: Chinese Academy of Agricultural Sciences
Xiuzhi Wei: Chinese Academy of Agricultural Sciences
Qican Cheng: Chinese Academy of Agricultural Sciences
Zhiwei Jia: Yazhou-Bay Science and Technology City
Xiaojiao Li: Yazhou-Bay Science and Technology City
Qiang Wang: Heilongjiang Academy of Agricultural Sciences
Yueqiang Wang: Jilin Academy of Agricultural Sciences
Wen Huang: Tonghua Academy of Agricultural Sciences
Chunyan Yang: Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences
Like Liu: Liaocheng University
Xing Wang: Jiangsu Xuhuai Regional Institute of Agricultural Sciences
Guangnan Xing: Nanjing Agricultural University
Guoyu Hu: Anhui Academy of Agricultural Sciences
Zhihui Shan: Oil Crops Research Institute, Chinese Academy of Agriculture Sciences
Ruizhen Wang: Crops Research Institute, Jiangxi Academy of Agricultural Sciences
Haiyan Li: Hainan Yazhou Bay Seed Laboratory
Hongyu Li: Chinese Academy of Agricultural Sciences
Tao Zhao: Chinese Academy of Agricultural Sciences
Jun Liu: Chinese Academy of Agricultural Sciences
Yuping Lu: Yazhou-Bay Science and Technology City
Xiping Hu: Beidahuang KenFeng Seed Co., Ltd, Binxi Economic Development Zone
Fanjiang Kong: Guangzhou University
Li-juan Qiu: Chinese Academy of Agricultural Sciences
Bin Liu: Chinese Academy of Agricultural Sciences

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract Shading in combination with extended photoperiods can cause exaggerated stem elongation (ESE) in soybean, leading to lodging and reduced yields when planted at high-density in high-latitude regions. However, the genetic basis of plant height in adaptation to these regions remains unclear. Here, through a genome-wide association study, we identify a plant height regulating gene on chromosome 13 (PH13) encoding a WD40 protein with three main haplotypes in natural populations. We find that an insertion of a Ty1/Copia-like retrotransposon in the haplotype 3 leads to a truncated PH13H3 with reduced interaction with GmCOP1s, resulting in accumulation of STF1/2, and reduced plant height. In addition, PH13H3 allele has been strongly selected for genetic improvement at high latitudes. Deletion of both PH13 and its paralogue PHP can prevent shade-induced ESE and allow high-density planting. This study provides insights into the mechanism of shade-resistance and offers potential solutions for breeding high-yielding soybean cultivar for high-latitude regions.

Date: 2023
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DOI: 10.1038/s41467-023-42608-5

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